IRLC (Inverted Repeat-lacking clade)

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Introduction

The Inverted Repeat-lacking clade or IRLC (Wojciechowski et al., 2000), so-called because it is uniquely marked by the loss of one copy of the large inverted repeat (approx. 25 kilobase) in the chloroplast genome (see below, under Characteristics), includes most members of Polhill's (1981) "temperate herbaceous group" of papilionoids. This group comprises all members of tribes Cicereae, Hedysareae, Trifolieae, and Fabeae (also known as Vicieae), as well as at least three genera, Afgekia Craib., Callerya Endl., and Wisteria Nutt., currently treated in tribe Millettieae (Schrire, 2005), nested within the paraphyletic tribe Galegeae (Polhill, 1994).

Polhill's "temperate herbaceous group" of tribes had been distinguished from other predominantly temperate tribes such as Thermopsideae (e.g., genera such as Baptisia, Thermopsis) by the accumulation of the non-protein amino acid canavanine, rather than alkaloids, in seeds. This group contains many of the familiar temperate and agriculturally important legumes such as alfalfa, clovers, lentils, chickpea, garden pea, vetches, as well as locoweeds, and ornamental "desert peas" and wisterias. The IRLC also includes a large number of model species such as Medicago truncatula (barrel medic), Medicago sativa (alfalfa), Pisum sativum (garden pea), Vicia faba (fava bean), and Trifolium repens (white clover), used for studies of symbiotic nitrogen fixation, root nodule development, legume development, genetics and genomics, and bacterial-plant coevolution.

Characteristics

The IRLC is dominated by often large, temperate genera such as Astragalus L., Hedysarum L., Medicago L., Oxytropis DC., Swainsona Salisb., and Trifolium L., which share a number of morphological characters including a predominantly herbaceous habit (annual and perennial), epulvinate compound leaves, stipules adnate to the petiole, base chromosome numbers of n = 7 or n = 8, and centers of greatest species diversity in Eurasia and North America (Polhill and Raven, 1981; Polhill, 1994), in addition to the loss of one copy of the inverted repeat in the chloroplast genome. This structural mutation in legumes (Palmer et al., 1987; Lavin et al., 1990) is particularly remarkable since the inverted repeat, which encodes a duplicate set of ribosomal RNA genes (structural RNA molecules used to make ribosomes which are part of the cell machinery for protein synthesis), is an evolutionary conserved feature of green algal and land plant chloroplast genomes (Palmer et al., 1988), and is known to be absent otherwise only from certain conifers (Strauss et al., 1988) and a few, specific genera in the angiosperm families Geraniaceae and Orobanchaceae (Downie and Palmer, 1992).

Discussion of Phylogenetic Relationships

The IRLC was the first clade within legumes essentially distinguished on the basis of a molecular synapomorphy, the loss of one copy of the 25-kb IR in the chloroplast genome. The monophyly of the IRLC has been consistently and strongly supported (e.g., 100% bootstrap proportions) in essentially all studies based on cladistic analyses of molecular data, including chloroplast DNA restriction fragment length polymorphisms (Lavin et al., 1990; Liston, 1995), nuclear rDNA ITS sequences (Sanderson and Wojciechowski, 1996) and chloroplast gene/intron sequences (Doyle et al., 1997; Käss and Wink, 1997; Hu et al., 2000; Kajita et al., 2001; Wojciechowski et al., 2004).

Within the IRLC, the so-called "IRLC millettioids", genera Afgekia, Callerya, and Wisteria (and possibly Endosamara) along with Glycyrrhiza of Galegeae form a paraphyletic grade at the base of the IRLC. Relationships among these lineages are currently not well-resolved or supported, a consequence most likely due to the lack of adequate sampling. Three well-supported subclades, the "Hedysaroid" clade, Galegeae sens. lat., and the "Vicioid" clade, comprise the remainder of the IRLC. The tribe Hedysareae (Polhill, 1994), recently expanded by Lock (2005) to include the genera Calophaca, Caragana, Halimodendron, and Alhagi formerly treated in Galegeae (Polhill, 1994) in addition to the large genera Hedysarum and Onobrychis, comprises the Hedysaroid clade. However, sampling within the Hedysaroid clade has been limited and relationships both within and among the 12 genera (and 400-450 species) remain poorly understood.

The Galegeae sens. lat. subclade of the IRLC consists of the majority of genera formerly treated in tribe Galegeae (sensu Polhill, 1994; Lock and Schrire, 2005) and include Astragalus, Chesneya, Oxytropis, Sutherlandia, Swainsona, Colutea, and Carmichaelia. With the exception of Astragalus and Oxytropis, all of these genera are distributed exclusively in Eurasia, Africa, or Australasia. Nested within this group is the well-supported "Astragalean" clade which includes the genus Astragalus, the largest genus of vascular plants with an estimated 2,500 species (plus a number of segregates), Oxytropis, and subtribe Colutinae (Wojciechowsk et al., 1999, 2000).

The Vicioid subclade of the IRLC includes many of the agriculturally important genera and model species such as Cicer, Medicago, Pisum, Trifolium, and Vicia. Within this subclade, the genus Parochetus (Trifolieae) is consistently resolved as the sister group to all other vicioid taxa; genus Galega forms the sister group to the monogeneric tribe Cicereae (Cicer), and together these taxa form the sister group to a clade that includes the tribes Trifolieae and Fabeae (formely known as Vicieae) (Steele and Wojciechowski, 2003; Wojciechowski et al., 2004). Results based on analyses of the matK gene (Steele and Wojciechowski, 2003) suggest the genus Trifolium ("clovers") is the sister group to the Fabeae rather than to remaining members of the tribe Trifolieae, but this position is still weakly supported and the subject of on-going investigation (e.g., see recent phylogeny of Trifolium; Ellison et al., 2006).

Liston, A. 1995. Use of the polymerase chain reaction to survey for the loss of the inverted repeat in the legume chloroplast genome. Pages 31-40 in Advances in legume systematics, part 7, Phylogeny (M. D. Crisp and J. J. Doyle, eds.). Royal Botanic Gardens, Kew, UK.

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